BN1842 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 1.1940e-05 1.0400e-02
Layer 4 1.2078e-05 4.5509e-04
Layer 2 3.3903e-05 5.9980e-02
Layer 5 8.9641e-05 2.1465e-03
Layer 6 1.1397e-03 1.2329e-02
WM 5.2218e-02 2.3533e-01
Layer 1 5.9795e-01 6.2489e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 2.1777 0.5608
MYO5A Layer 4 2.3867 0.5605
SV2A Layer 5 2.2227 0.5565
DCLK1 Layer 3 2.5840 0.5534
HK1 Layer 4 2.1514 0.5502
BMERB1 Layer 4 2.2578 0.5488
MGST3 Layer 4 2.1016 0.5477
STMN2 Layer 5 2.2461 0.5471
CPLX1 Layer 3 2.7070 0.5459
SATB1 Layer 4 2.4297 0.5456
MOAP1 Layer 4 2.3105 0.5433
EPHB6 Layer 4 2.5928 0.5425
GNB1 Layer 4 1.9541 0.5385
ELAVL4 Layer 4 2.6836 0.5378
ATP1A3 Layer 4 2.3125 0.5368
BEX4 Layer 3 1.9629 0.5368
NRSN1 Layer 5 2.4238 0.5342
RAB6A Layer 3 2.1719 0.5327
NGRN Layer 4 2.0723 0.5320
ISCA1 Layer 4 2.2461 0.5311
NRN1 Layer 4 2.4297 0.5307
CLSTN3 Layer 4 2.5928 0.5300
SYT4 Layer 3 2.2773 0.5298
CNTNAP2 Layer 4 3.2715 0.5294
MDH1 Layer 3 2.1445 0.5284
SNCB Layer 3 2.1719 0.5272
SNX10 Layer 5 2.2461 0.5268
PGK1 Layer 4 2.2295 0.5265
NAPB Layer 3 2.1777 0.5262
DYNC1H1 Layer 4 2.2617 0.5258
NEFL Layer 3 2.0957 0.5255
NDRG4 Layer 3 2.1582 0.5254
PFN2 Layer 4 2.1875 0.5249
NDUFA5 Layer 3 2.1875 0.5249
SCG5 Layer 4 2.1777 0.5236
FBXW7 Layer 5 2.1289 0.5234
GHITM Layer 4 2.1875 0.5229
PRDX5 Layer 3 2.1094 0.5225
ATP5MPL Layer 3 1.9766 0.5222
GPI Layer 2 2.0859 0.5217
SYNGR3 Layer 5 2.2715 0.5215
SCAMP1 Layer 3 2.1543 0.5214
TAGLN3 Layer 3 2.1445 0.5211
ATP1A1 Layer 3 2.1289 0.5210
GOT1 Layer 4 2.2598 0.5207
TTC9B Layer 3 2.3184 0.5205
CDK14 Layer 4 2.4814 0.5195
NAP1L3 Layer 4 2.4863 0.5190
PRKAR1B Layer 3 2.1094 0.5186
RGS4 Layer 4 2.0957 0.5186

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1842
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1842_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1842/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1842/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1842/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1842/report/PD/BN1842_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1842/report/PD/BN1842_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 08:28:12
  • Number of Processes: 10
  • Spending Time: 0h 3m